Defence Minister Peter Dutton has defended overruling senior officials and allowing special forces troops to keep their meritorious unit citations from Afghanistan despite credible allegations of war crimes.

Mr Dutton was warned failing to strip the unit of its citation would harm the reputation of the Australian Defence Force at home and abroad.

But he defied the briefing from his department and stepped in to stop members of the Special Operations Task Group from being stripped of the military honours.

“The job of a minister is to look at the options presented, to look at the information provided to me, and my job as minister is to make the decision,” Mr Dutton told Sky News on Wednesday.

“I took the decision I thought was in the best interests of our country and in the best interest of the men and women of the Australian Defence Force.”

The move to revoke the unit citation was a key recommendation of the Brereton war crimes inquiry, which found credible allegations special forced troops committed 39 murders in Afghanistan.

Mr Dutton said he did not want the actions of a small group of soldiers to spoil the reputation of the vast majority of special forces troops who served with distinction in the Middle East.

Only those who are convicted of crimes will be stripped of their honours.

“There are thousands of men and women who served with great honour and distinction in the Afghanistan campaign and in Iraq as well over the course of the last two decades and I am not going to dishonour their service,” he said.

“I am going to say to the one per cent of people who do the wrong thing that if you are found to be guilty in a court of law then there will be consequences that you face.

“But for the vast majority of our men and women of the Australian Defence Force, they have done incredible work in our name, they have stopped terrorist attacks in our country and in other parts of the west, and we should be eternally grateful for their service.”

-AAP